- Oniwakamaru's death, dying happily that Fuu wasn't afraid of him, and that he wasn't alone.
- Shin's death in episode seven. He broke the law in an effort to save his mother's life and was killed for it.
- Mugen's near death flashbacks in the second "Misguided Miscreants" episode. It wouldn't be nearly as potent if it weren't for the hauntingly beautiful song that plays during it all.
- Pretty much everything about Okuru.
- Jin parting ways with Shino at the end of "Gamblers and Gallantry." The score for that scene, Nujabes' "Counting Stars", drives it all home.
- Sara's death. The fact that it actually gets an emotional reaction from Mugen only served to add to the tragedy. In fact, Sara period.
- The revelation of what really happened to Jin's kendo master: Master Mariya had cut a deal with the shogunate assassins that Jin, as heir presumptive to the dojo, opposed. Mariya was ordered to kill his star pupil/adopted son to prove his loyalty and attacked Jin in his bedroom. Jin was the better swordsman and struck Mariya fatally before he even realized the identity of his attacker. And in the moment when he does realize, his entire world crashes down around his ears and you can hear it in his voice.
- The death of Fuu's father, shortly after finally reuniting with her.
- The bittersweet finale doubles as a Heartwarming Moment and a massive tearjerker as the three split up, confident that they will all meet again.
Tear Jerker / Samurai Champloo